Depending on how exactly the tools try to accomplish their task, they might work, might not work or might even damage the FS.
The latter will happen if they access the disk on block level without noticing that the FS in use is not understood by them.
As long as they depend on using the file level to erase the data it'll be safe at least.
When the FS makes no attempt to save a file from being inadvertently overwritten/destroyed it will also work - I'm not aware of any Amiga FS being able to do so, but I haven't used ProFS or SFS yet. Obviously the FS in question would come with tools allowing you to recover overwritten data, otherwise it's very unlikely that such a feature exists.
(The file level works by opening the file for modification, overwriting the contents with arbitrary data or certain bit patterns, possibly several times and finally deleting the file. A file system with overwrite protection creates a backup during this process, i.e. stores the new data in a previously empty area of the disk while keeping the old data in the background. E.g. Novell Netware does this in some scenarios.)
